SchmitzStreitsLAB

An Asgard Archaeon (Lokiarchaeum ossiferum) growing and retracting its arms

Preprint: Systematic discovery of TIR-based immune signaling systems in bacteria

Conservation of TIR-derived signals accross the tree of life! We found bacterial TIR immune systems that signal via canonical cADPR (like in humans) and 2'cADPR (a plant immune signal).

Documented 11 Thoeris types

Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes - Nature Microbiology Evading infection in Cellulophaga baltica comes with cellular changes that alter carbon cycling, metabolite secretion and sedimentation rates.

#NewResearch

Evading infection in Cellulophaga baltica comes with cellular changes that alter carbon cycling, metabolite secretion and sedimentation rates.

#MicroSky #EnvMicro 🦠🌐 @sullivan-lab.bsky.social @howard-varona.bsky.social

www.nature.com/articles/s41...

A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models - Nature Microbiology HRGM2 is a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut micro...

#Resource

HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes.

#MicroSky #MicrobiomeSky 🦠💻

www.nature.com/articles/s41...

a man walking in a field with an umbrella ALT: a man walking in a field with an umbrella

Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea

Let’s wrap things up: Open and closed hypernucleosomes in Asgard archaea Asgard archaea are widely considered the closest living relatives of eukaryotes. In this issue of Molecular Cell, Ranawat et al. report high-resolution structures of hypernucleosomes formed by the hodarchaeal HHoB histone, disclosing open and closed chromatin conformations.

Let’s wrap things up: Open and closed hypernucleosomes in Asgard archaea

🧬🛡️How are new immune mechanisms created?

We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!

doi.org/10.1073/pnas...

The mechanism of Lamassu, an abundant bacterial immune system, is now solved

Lamassu evolved from a DNA repair complex

Beautiful study from the Patel, Bernheim and Sternberg labs

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

#NatMicroPicks

IScream phages in gut 🧬🦠

Long-read metagenomics reveals dynamic prophage integration, cross-family host jumps, and IS30-driven phage mobilization in the human gut

#MicroSky #MicrobiomeSky

www.nature.com/articles/s41...

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

#NatMicroPicks

Editing gut microbiota in vivo! 🔧🧬🦠

MetaEdit enables precise in vivo CRISPR-based editing of native gut bacteria, integrating new pathways at single-nucleotide resolution

#MicroSky #SynBio

www.science.org/doi/10.1126/...

Impact of Small RNA Sponges on Regulatory RNA Networks in Bacteria Decades of research into the noncoding transcriptome have unveiled a complex, multilayered web of molecular interactions that govern gene expression, protein synthesis, and cellular function, challeng...

Impact of Small RNA Sponges on Regulatory RNA Networks in Bacteria

#microsky

www.annualreviews.org/content/jour...

ZAK activation at the collided ribosome - Nature The kinase ZAK is activated at collided ribosomes to mediate the ribotoxic stress response.

Check out our latest work on how collided ribosomes activate the MAP3K ZAK! 💫

www.nature.com/articles/s41...

A fun collaboration with @beckmannlab.bsky.social @doubleshuang.bsky.social

YouTube video by CMFI - Cluster of Excellence WAAW - World Antimicrobial Awareness Week

🌍 World Antimicrobial Awareness Week 2025 🦠

Antimicrobial resistance threatens global health.
Unnecessary antibiotic use accelerates resistance and makes infections harder to treat.

Use antibiotics responsibly and help raise awareness.

Act now!

youtu.be/_Qy3aTKiVLE

#WWAW2025 #AMR #GoBlue

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

#NatMicroPicks

CRISPR Metagenome Engineering! 🦠🔧🧬

MetaEdit enables precise genetic editing of native gut bacteria in mice.

#MicroSky #SynBio

www.science.org/doi/10.1126/...

Job advertisement

Are you looking to establish yourself as a scientific group leader? BRIC is recruiting 1-2 junior group leaders to join our research centre in the heart of Copenhagen.
See more at www.bric.ku.dk

Please repost and get in touch if you are curious.

List of available cultures

Ecoli cells (Dapi, on left) expressing bacterial (center) and archaeal 16S rRNA.

Clone-FISH paper out: Manuscript/resource alert #microsky 🦠 We present a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 17 yet uncultured ones.

the sun is shining through the clouds in the sky above the ocean ALT: the sun is shining through the clouds in the sky above the ocean

Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis www.nature.com/articles/s41...
this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

#Archaea, #DPANN, #phylogenetic_reconciliation
New preprint online!
www.biorxiv.org/content/10.1...

MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony.

Or from a single dish of HEK cell culture in the case of two membrane proteins.

Out in Nature Methods now! lnkd.in/gpyBSceg

Wonderful collaboration with the Efremov lab.

ECR connection: Meet Meren when you need to A means for ECRs to get advice from a senior scientist outside of their support network

Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.

Here is a blog that explains my motivation for this and how to schedule a meeting:

merenlab.org/2025/11/16/E...

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PhD /PostDoc positions available. Exploration of physiological functions of the cell fusogen Fusexin1 in Archaea.
In a collaborative project between the Albers lab (Freiburg) and the Podbilewicz lab (Technion) starting in January 2026.

An Asgard archaeon with internal membrane compartments The emergence of eukaryotes from a merger between an archaeon and a bacterial cell ~two billion years ago involved a profound change in cellular organisation. While the order in which different featur...

An Asgard archaeon containing internal membrane compartments!! 😯
This will reshape our understanding of how the eukaryotic endomembrane system originated.
Congrats to @buzzbaum.bsky.social, @tbharat-lab.bsky.social and all ppl involved!
www.biorxiv.org/content/10.1...

Modulation of archaeal hypernucleosome structure and stability by Mg2+ DNA-wrapping histone proteins play a central role in chromatin organization, gene expression and regulation in most eukaryotes and archaea. While the …

New article online: Modulation of archaeal hypernucleosome structure and stability by Mg2+

In this work, we dissect the effects of Mg2+ on hypernucleosomes formed by the canonical histones from M. fervidus (HMfA and HMfB) and T. kodakarensis (HTkA and HTkB).

www.sciencedirect.com/science/arti...

Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides

tinyurl.com/ch3damp

We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity

Revealed by the amazing Ilya Osterman. See his thread below👇

True!

DNA scientist James Watson has a remarkably long history of sexist, racist public comments “People say it would be terrible if we made all girls pretty,” he said in 2003. “I think it would be great.”

Hey folks, as news of Watson's demise spreads, please don't set aside his weighty legacy of misogyny and racism. He was truly among the worst of us. www.vox.com/2019/1/15/18...

Rosalind Franklin and the damage of gender harassment Spurred by a recent report on sexual harassment in academia, our columnist revisits a historical case and reflects on what has changed—and what hasn’t

Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).

Soon available in my group: 1 PhD position to investigate prokaryotic histones. See our recent work that highlights the existence and diversity of prokaryotic histones (e.g. Schwab et al., TIBS, 2025; Schwab et al., Nat Comm, 2024; Hu et al., Nucl Acids Res, 2024). Please DM for informal enquiries.